Sentence examples for experimental conformation from inspiring English sources

Therefore, the accuracy of a conformer model generated by OMEGA was evaluated using the minimum RMSD and the maximum ST values between the experimental conformation and a single theoretical 3-D conformation in the conformer model.

Left: generated binding mode of indomethacin (blue, balls and sticks) in the PDB: 4COX compared to its experimental conformation (black sticks).

In the study by Hawkins et al.[18], an RMSD value of 1.25 Å or less was employed as the definition of a "close" reproduction of the experimental conformation.

Also note that this interpretation is consistent with the fact that the 90% of the conformer models considered in this study have RMSD accuracies better than 1.1 Å, which is much tighter than the common upper bound (RMSD 2.0 Å) for successful reproduction of an experimental conformation in molecular docking, as mentioned above.

However, we note, that the effects of the parallel sites on properties such as wavelength shifts needs experimental conformation.

Additionally, the inhibitor cocrystallized in the mouse experimental structure (ligand named QZ59, pdb code 3G60) was redocked into the homology model (simulation 5) to evaluate the capacity of the model to reproduce the mouse experimental conformation.

Although the experimental conformations are very similar, the corresponding differences in conformational energies, ΔΔ Eintra < 1.5 kJ mol 1, are still comparable to the calculated energy differences between pairs of polymorphs.

To make the PIXEL crystal energies of different Pbtl polymorphs comparable with one another, we have estimated the intramolecular energy penalties (∆E intra) of their experimental conformations (Additional file 1: Table S13) with respect to the global conformational energy minimum.

Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 Å to their respective experimental conformations.

Nevertheless, MODPEP also failed to give models close to the experimental conformations for some peptides even when an ensemble of 1000 conformations were generated (Fig. 6).

The ϕ values for all previously reported experimental conformations lie within the narrow range of 0° ± 5°, indicating that the ethyl orientation perpendicular to the pyrimidinetrione ring might be the preferred one in the solid state of Pbtl.